There's now also a bug report to follow. The bug has been fixed, if you still see this, I'd report a new bug (unless it's happening with windows that can only be resized in fixed sized steps like gnome-terminal).

@Ike: np, if you want to change/disable the window, it's now also part of the theme (right above the padding lines) - except for the color, which still follows the window decorator plugin in Compiz.
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htorqueJan 30 '11 at 21:09